From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 26 2013 - 17:39:30 CDT

If the only difference is hydrogens, then trying a variation of the
"not hydrogens" keywords should do it. You probably don't want to
include hydrogens in any alignment anyway...

Cheers,
  John

On Tue, Mar 26, 2013 at 03:38:11PM -0700, Yarrow Madrona wrote:
> Thanks,
>
> The problem is that one HEME residue has hydrogens and the other doesn't.
> I guess I can remove the hydrogens or say something like "resname HEME and
> not hydrogens"?
>
> -Yarrow
>
> > Hi,
> > As the error message indicates, the number of atoms that results from
> > the in the alignment selection text must be exactly the same for the two
> structures (or frames) you want to align. If you're getting differing
> numbers of atoms from the same selection text, then you need to choose
> an atom selection that will result in the same atom count, and more
> generally
> > the same atoms (matching parts of related structures) between the two
> molecules.
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> > On Tue, Mar 26, 2013 at 12:19:48PM -0700, Yarrow Madrona wrote:
> >> Hi,
> >> I know this is a basic question but I am having trouble alining two
> very
> >> similar molecules (98% seq homology) based on a heme selection. Each time,
> >> I get the following complaint,
> >> measure fit: selections must have the same number of atoms
> >> A similar result happens when I try to use the RMSD caclulator
> >> extension.
> >> Any help would be appreciated. Thank you.
> >> --
> >> Yarrow Madrona
> >> Graduate Student
> >> Molecular Biology and Biochemistry Dept.
> >> University of California, Irvine
> >> Natural Sciences I, Rm 2403
> >> Irvine, CA 92697
> >> --
> >> Yarrow Madrona
> >> Graduate Student
> >> Molecular Biology and Biochemistry Dept.
> >> University of California, Irvine
> >> Natural Sciences I, Rm 2403
> >> Irvine, CA 92697
> > --
> > NIH Center for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> > http://www.ks.uiuc.edu/Research/vmd/
>
>
> --
> Yarrow Madrona
>
> Graduate Student
> Molecular Biology and Biochemistry Dept.
> University of California, Irvine
> Natural Sciences I, Rm 2403
> Irvine, CA 92697
>
>
>
>

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/